In Silico Study of Coumarins: Wedelolactone as a Potential Inhibitor of the Spike Protein of the SARS-CoV-2 Variants

Table 2

Binding interaction analysis of the best-docked coumarins with spike proteins of SARS-CoV-2 variants among the selected top 10 coumarins.

SARS-CoV-2 variant S-RBDs	Best-dockedcoumarins	Binding energy (kcal/mol)	Interacting residues	Interaction types	Interacting distance (Å)
Wild-type variant; PDB ID: 6M0J	Inophyllum B	−7.4	GLN 498	Conventional H bond	2.23
			ASN 501	Conventional H bond	2.86
			ARG 403	Pi-cation	4.91
			TYR 505	Pi-Pi T-shaped	4.91
Alpha variant; PDB ID: 7EKF	Inophyllum D	−7.5	SER 494	Conventional H bond	2.26
			TYR 449	Pi-alkyl	5.17
			TYR 501	Pi-Pi stacked (Pi-Pi T-shaped)	5.60, (4.94)
			TYR 505	Pi-Pi stacked	3.77
Beta variant; PDB ID: 7EKG	Soulattrolide	−7.2	GLN 493	Conventional H bond	2.18
			SER 494	Conventional H bond	2.82
			PHE 490	Pi-Pi stacked (Pi-alkyl)	4.60, 4.90, (4.77)
			LYS 484	Alkyl	4.81
Gamma variant; PDB ID: 7EKC	Inophyllum E	−7.8	SER 494	Conventional H bond	2.32
			GLN 493	Carbon H bond	3.51
			LYS 484	Pi-Pi stacked	4.18, 5.52
			PHE 490	Pi-alkyl	4.99
Delta variant; PDB ID: 7WBQ	Soulattrolide	−7.8	GLN 498	Conventional H bond	2.73
			ASN 501	Conventional H bond	2.94
			ARG 403	Pi-cation	4.03
			TYR 505	Pi-Pi T-shaped	5.72
			TYR 449	Carbon H bond	3.07